# source(here::here("networks/Manhattan_plot.R"))
system(paste("RScript",
here::here("networks/Manhattan_plot.R"),
"-p networks/MS.pvals.out",
"-o networks/ms_manhattan_plot.pdf"
)
)
system(paste("RScript",
here::here("networks/Manhattan_plot.R"),
"-p networks/HT.pvals.out",
"-o networks/ht_manhattan_plot.pdf"
)
)
# source(here::here("networks/qqplot.R"))
system(paste("RScript",
here::here("networks/qqplot.R"),
"-p networks/MS.pvals.out",
"-o networks/ms_qqplot.pdf"
)
)
system(paste("RScript",
here::here("networks/qqplot.R"),
"-p networks/HT.pvals.out",
"-o networks/ht_qqplot.pdf"
)
)
MS has more power (seen by more significant findings)
The above image shows the full network. After running analysis in cytoscape, the resulting summary information and plots were produced:
Summary Statistics
Number of nodes: 8960
Number of edges: 27724
Avg. number of neighbors: 6.363
Network diameter: 13
Network radius: 7
Characteristic path length: 4.382
Clustering coefficient: 0.088
Network density: 0.001
Network heterogeneity: 2.063
Network centralization: 0.033
Connected components: 164
Analysis time (sec): 34.270
- show degree
distribution - scale free,
#source(here::here("networks/Pathway_permutations.R"))
system(paste("RScript",
here::here("networks/Pathway_permutation.R"),
"-p networks/parent_PPI.sif",
"-o networks/q4_pathway_permutation.pdf"
)
)
Looking at the top GO term enrichments by BINGO analysis (above) immune system related processes clearly emerge as important.
#source(here::here("networks/Pathway_permutations.R"))
system(paste("RScript",
here::here("networks/Pathway_permutation.R"),
"-p networks/Directed_PPI.sif",
"-o networks/q7_pathway_permutation.pdf"
)
)
The null hypothesis to test is: The number of controllable genes in the MS-associated first order network is consistent with random sampling of controllable genes from the full directed network.
# total number of nodes in the MS associated gene first order network
# this is k in the hypergeometric parameters
k = 546
# is the total number of controllable nodes in the network
# i.e. dispensible + indispensible
m = 3677 - 8 # is the number of unlabelled nodes
# n is the total number of nodes in the directed network
n = 6338- m
# then the value to test for is the number of controllable
# ms associated genes
q = 317
phyper(k= k,
lower.tail = F,
m = m,
n = n,
q = q)
## [1] 0.4493194
This p-value suggest that MS-associated genes are not enriched for controllable genes. This is unsurprising given the proportion of controllable genes out of the MS-associated genes (317/549 \(\approx\) 58%) is very similar to the proportion of controllable gene in the entire directed network (3667/6338).